Structure of Organic Molecules

Carbon skeleton and valence states

The chemical nature of organic substances is based on the unique characteristics of carbon. In stable structures, this element is always in a tetravalent state (IV). The only exceptions are carbenes—short-lived and extremely active chemical reaction intermediates. In carbenes, carbon is divalent (II) and exists as a biradical or a structure with a free electron pair.

The foundation of any organic molecule is its carbon skeleton—a chain of bonded carbon atoms. The outstanding strength of the single C–C bond (347 kJ/mol), significantly exceeding the strength of analogous bonds between silicon, nitrogen, or oxygen atoms, ensures the existence of stable molecules of any size. The structure of the skeleton can be:

• Linear (unbranched);
• Branched (with side chains);
• Cyclic (simple closed rings or rings with additional branches).

Carbon hybridization and bond geometry

The spatial arrangement of atoms around carbon depends on its hybridization state. There are three main types that determine the geometry of the molecule:

Unsaturated bonds and electronegativity

A special role is played by molecules with carbon in $sp^2$- and $sp$-states, which are called unsaturated compounds. They contain multiple bonds, the feature of which is the presence of a mobile electronic $\pi$-pair. Unlike rigidly fixed $\sigma$-bonds, $\pi$-electrons are easily displaced under the influence of neighboring atoms (they are polarized), which gives such compounds high reactivity.

In addition to hydrogen and carbon, molecules often contain heteroatoms: oxygen, nitrogen, halogens, and sulfur. Since the electronegativity of O, N, and halogens is higher than that of carbon, bonds with them become polar. Electron density is displaced, forming partial positive ($\delta+$) and negative ($\delta-$) charges. Sulfur, on the other hand, has a lower electronegativity than carbon. The presence of such charges critically influences the types of reactions the molecule will undergo.

Structural formulas and molecular fragments

To describe the structure, different types of formulas are used. For example, for propane, the molecular formula shows only the composition ($C_3H_8$), the condensed structural formula shows bonds between carbons ($CH_3-CH_2-CH_3$), and the stereochemical formula reflects real stereochemistry. Graphic (skeletal) formulas in the form of broken lines are widely used, where hydrogen atoms and carbon symbols are omitted.

When constructing structures, it is critically important to distinguish true isomerism (when shifting a functional group creates a new molecule with different properties) from projections, where the exact same molecule is simply depicted from a different angle (e.g., a group is "flipped" downwards).

Functionally, the molecule is divided into components:

1. Hydrocarbon radicals: fragments made of C and H (methyl $-CH_3$, ethyl $-C_2H_5$).
2. Functional groups: regions with heteroatoms where most reactions take place. They determine the class of the substance: hydroxyl $-OH$ is characteristic of alcohols, carboxyl $-COOH$ imparts acidic properties, and the amino group $-NH_2$ imparts basic properties.

Class and exam questions

What else to study on this topic

• Features of conjugated double bonds
• Properties of carbenes as short-lived particles
• Mechanisms of $\pi$-bond polarizability
• Rules for constructing skeletal graphic formulas
• Influence of heteroatom electronegativity on chemical activity

Other topics in "Chapter 14. Theoretical Foundations of Organic Chemistry"

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